RIOX2

Chr 3

ribosomal oxygenase 2

Also known as: JMJD10, MDIG, MINA, MINA53, NO52, ROX

NCBI Gene: 84864 ENSG00000170854 UniProt: Q8IUF8 OMIM: 612049

RIOX2 encodes an oxygenase that demethylates histone H3K9me3 to increase ribosomal RNA expression and hydroxylates ribosomal protein L27a, playing a key role in ribosome biogenesis and cell growth. Mutations cause autosomal recessive intellectual developmental disorder with short stature and variable brain malformations. The gene shows very high constraint against loss-of-function variants, indicating that complete loss of function is likely incompatible with normal development.

OMIM ResearchSummary from RefSeq, UniProt

MINA is a c-Myc (MYC; MIM 190080) target gene that may play a role in cell proliferation or regulation of cell growth. (Tsuneoka et al., 2002 [PubMed 12091391]; Zhang et al., 2005 [PubMed 15897898]).[supplied by OMIM, May 2008]

OMIM ResearchGenerating clinical summary…

LOEUF 1.07

Clinical Summary— RIOX2

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

86 VUS of 103 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.07LOEUF

pLI 0.000

Z-score 1.31

OE 0.70 (0.46–1.07)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.05Z-score

OE missense 0.99 (0.89–1.10)

253 obs / 255.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.70 (0.46–1.07)

0≤0.351.4

Missense OE?0.99 (0.89–1.10)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 15 / 21.6Missense obs/exp: 253 / 255.5Syn Z: -0.18

ClinVar Variant Classifications

103 submitted variants in ClinVar

ClinVar

Classification Summary

VUS86

Likely Benign4

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	86	86
Likely Benign	4	4
Benign	0	0
Total	90	90

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

10 pathogenic / likely-pathogenic (of 21) ClinVar copy-number / structural variants overlap RIOX2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →